EHV-1 TES dynamics
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only output)
TES dynamics
Those reads were counted only, where the 3-prime adapters were “correct” (according to LoRTIA)
Statistics of counts
Difference from mean
Varcoeff
Clustering of samples
## Bootstrap (r = 0.49)... Done.
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## Bootstrap (r = 0.79)... Done.
## Bootstrap (r = 0.89)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.09)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.3)... Done.
## Bootstrap (r = 1.38)... Done.
The sample 48h_3 stands out!
Filtering of samples
Clustering of genes into de-novo clusters using hierarchial clustering
Cluster memberships
## Bootstrap (r = 0.5)... Done.
## Bootstrap (r = 0.58)... Done.
## Bootstrap (r = 0.69)... Done.
## Bootstrap (r = 0.77)... Done.
## Bootstrap (r = 0.88)... Done.
## Bootstrap (r = 1.0)... Done.
## Bootstrap (r = 1.08)... Done.
## Bootstrap (r = 1.19)... Done.
## Bootstrap (r = 1.27)... Done.
## Bootstrap (r = 1.38)... Done.Optimal number of clusters
Find the optimal number of clusters to cut the tree at and calculate
Clustering statistics: Cluster number: 5
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF4 1.0000000 1.0000000 1.0000000
## 3: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 4: 1 ORF9 1.0000000 1.0000000 1.0000000
## 5: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 6: 1 ORF17 1.0000000 1.0000000 1.0000000
## 7: 1 ORF18 1.0000000 1.0000000 1.0000000
## 8: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 9: 1 ORF30 1.0000000 1.0000000 1.0000000
## 10: 1 ORF31 1.0000000 1.0000000 1.0000000
## 11: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 12: 1 ORF38 1.0000000 1.0000000 1.0000000
## 13: 1 ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 14: 1 ORF63 1.0000000 1.0000000 1.0000000
## 15: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 16: 1 ORF65_1 1.0000000 1.0000000 1.0000000
## 17: 1 ORF68, ORF67_1 1.0000000 1.0000000 1.0000000
## 18: 1 ORF69, ORF70 1.0000000 1.0000000 1.0000000
## 19: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 20: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 21: 2 ORF2 0.7048446 0.8666192 0.8075293
## 22: 2 ORF3 0.7048446 0.8666192 0.8075293
## 23: 2 ORF8 0.7048446 0.8666192 0.8075293
## 24: 2 ORF12, ORF13, ORF14 0.7048446 0.8666192 0.8075293
## 25: 2 ORF22 0.7048446 0.8666192 0.8075293
## 26: 2 ORF23 0.7048446 0.8666192 0.8075293
## 27: 2 ORF24 0.7048446 0.8666192 0.8075293
## 28: 2 ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 29: 2 ORF28, ORF29 0.7048446 0.8666192 0.8075293
## 30: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 31: 2 ORF36 0.7048446 0.8666192 0.8075293
## 32: 2 ORF37 0.7048446 0.8666192 0.8075293
## 33: 2 ORF39 0.7048446 0.8666192 0.8075293
## 34: 2 CTO 0.7048446 0.8666192 0.8075293
## 35: 2 ORF40 0.7048446 0.8666192 0.8075293
## 36: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 37: 2 ORF44 0.7048446 0.8666192 0.8075293
## 38: 2 ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 39: 2 ORF62, ORF61, ORF60,ORF59 0.7048446 0.8666192 0.8075293
## 40: 2 ORF66_1 0.7048446 0.8666192 0.8075293
## 41: 3 ORF18, ORF17, ORF16, ORF15 0.9968786 0.9990302 0.9826369
## 42: 3 ORF19 0.9968786 0.9990302 0.9826369
## 43: 3 ORF52 0.9968786 0.9990302 0.9826369
## 44: 3 ORF57, ORF58 0.9968786 0.9990302 0.9826369
## 45: 3 ORF71, ORF72, ORF73 0.9968786 0.9990302 0.9826369
## 46: 4 ORF53, ORF54 0.2153731 0.6088215 0.6060342
## 47: 5 ORF64_1 0.2097334 0.6269125 0.5728833
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 7: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 8: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 9: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 16: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 17: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 18: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 19: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 20: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 28: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 29: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 30: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 31: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 32: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 33: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 34: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 35: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 36: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 37: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 38: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 39: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 40: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 41: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 42: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 43: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 44: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 45: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 46: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 47: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## se.si se.au se.bp v c pchi
## [1] "ORF69, ORF70" "ORF37, ORF36, ORF35, ORF35.5"## [1] 2## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF12, ORF13, ORF14"
## [5] "ORF22" "ORF23"
## [7] "ORF24" "ORF27, ORF26, ORF25"
## [9] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [11] "ORF36" "ORF37"
## [13] "ORF39" "CTO"
## [15] "ORF40" "ORF41, ORF42, OF43"
## [17] "ORF44" "ORF45, ORF46"
## [19] "ORF62, ORF61, ORF60,ORF59" "ORF66_1"
## [21] "ORF53, ORF54" "ORF64_1"## [1] 22Clustering statistics: Cluster number: 6
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF9 1.0000000 1.0000000 1.0000000
## 4: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 5: 1 ORF17 1.0000000 1.0000000 1.0000000
## 6: 1 ORF18 1.0000000 1.0000000 1.0000000
## 7: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 8: 1 ORF30 1.0000000 1.0000000 1.0000000
## 9: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 10: 1 ORF38 1.0000000 1.0000000 1.0000000
## 11: 1 ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 12: 1 ORF63 1.0000000 1.0000000 1.0000000
## 13: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 14: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 15: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 16: 2 ORF2 0.7048446 0.8666192 0.8075293
## 17: 2 ORF3 0.7048446 0.8666192 0.8075293
## 18: 2 ORF8 0.7048446 0.8666192 0.8075293
## 19: 2 ORF12, ORF13, ORF14 0.7048446 0.8666192 0.8075293
## 20: 2 ORF22 0.7048446 0.8666192 0.8075293
## 21: 2 ORF23 0.7048446 0.8666192 0.8075293
## 22: 2 ORF24 0.7048446 0.8666192 0.8075293
## 23: 2 ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 24: 2 ORF28, ORF29 0.7048446 0.8666192 0.8075293
## 25: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 26: 2 ORF36 0.7048446 0.8666192 0.8075293
## 27: 2 ORF37 0.7048446 0.8666192 0.8075293
## 28: 2 ORF39 0.7048446 0.8666192 0.8075293
## 29: 2 CTO 0.7048446 0.8666192 0.8075293
## 30: 2 ORF40 0.7048446 0.8666192 0.8075293
## 31: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 32: 2 ORF44 0.7048446 0.8666192 0.8075293
## 33: 2 ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 34: 2 ORF62, ORF61, ORF60,ORF59 0.7048446 0.8666192 0.8075293
## 35: 2 ORF66_1 0.7048446 0.8666192 0.8075293
## 36: 3 ORF4 0.9968786 0.9990302 0.9826369
## 37: 3 ORF31 0.9968786 0.9990302 0.9826369
## 38: 3 ORF65_1 0.9968786 0.9990302 0.9826369
## 39: 3 ORF68, ORF67_1 0.9968786 0.9990302 0.9826369
## 40: 3 ORF69, ORF70 0.9968786 0.9990302 0.9826369
## 41: 4 ORF18, ORF17, ORF16, ORF15 0.2153731 0.6088215 0.6060342
## 42: 4 ORF19 0.2153731 0.6088215 0.6060342
## 43: 4 ORF52 0.2153731 0.6088215 0.6060342
## 44: 4 ORF57, ORF58 0.2153731 0.6088215 0.6060342
## 45: 4 ORF71, ORF72, ORF73 0.2153731 0.6088215 0.6060342
## 46: 5 ORF53, ORF54 0.2097334 0.6269125 0.5728833
## 47: 6 ORF64_1 0.9902010 0.9978135 0.9076866
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 7: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 8: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 9: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 16: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 17: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 18: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 19: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 20: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 28: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 29: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 30: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 31: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 32: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 33: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 34: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 35: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 36: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 37: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 38: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 39: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 40: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 41: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 42: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 43: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 44: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 45: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 46: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 47: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## se.si se.au se.bp v c pchi
## [1] "ORF74, ORF75, ORF76, ORF67 _2" "ORF37, ORF36, ORF35, ORF35.5"## [1] 2## [1] "ORF2" "ORF3"
## [3] "ORF8" "ORF12, ORF13, ORF14"
## [5] "ORF22" "ORF23"
## [7] "ORF24" "ORF27, ORF26, ORF25"
## [9] "ORF28, ORF29" "ORF37, ORF36, ORF35, ORF35.5"
## [11] "ORF36" "ORF37"
## [13] "ORF39" "CTO"
## [15] "ORF40" "ORF41, ORF42, OF43"
## [17] "ORF44" "ORF45, ORF46"
## [19] "ORF62, ORF61, ORF60,ORF59" "ORF66_1"
## [21] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [23] "ORF52" "ORF57, ORF58"
## [25] "ORF71, ORF72, ORF73" "ORF53, ORF54"## [1] 26Clustering statistics: Cluster number: 7
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF9 1.0000000 1.0000000 1.0000000
## 4: 1 ORF10, ORF11 1.0000000 1.0000000 1.0000000
## 5: 1 ORF17 1.0000000 1.0000000 1.0000000
## 6: 1 ORF18 1.0000000 1.0000000 1.0000000
## 7: 1 ORF22, ORF21, ORF20 1.0000000 1.0000000 1.0000000
## 8: 1 ORF30 1.0000000 1.0000000 1.0000000
## 9: 1 ORF32, ORF33, ORF34 1.0000000 1.0000000 1.0000000
## 10: 1 ORF38 1.0000000 1.0000000 1.0000000
## 11: 1 ORF48, ORF49, ORF50, ORF51 1.0000000 1.0000000 1.0000000
## 12: 1 ORF63 1.0000000 1.0000000 1.0000000
## 13: 1 NOIR_1 1.0000000 1.0000000 1.0000000
## 14: 1 ORF74, ORF75, ORF76, ORF67 _2 1.0000000 1.0000000 1.0000000
## 15: 1 NOIR_2 1.0000000 1.0000000 1.0000000
## 16: 2 ORF2 0.7048446 0.8666192 0.8075293
## 17: 2 ORF8 0.7048446 0.8666192 0.8075293
## 18: 2 ORF23 0.7048446 0.8666192 0.8075293
## 19: 2 ORF24 0.7048446 0.8666192 0.8075293
## 20: 2 ORF27, ORF26, ORF25 0.7048446 0.8666192 0.8075293
## 21: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 22: 2 ORF36 0.7048446 0.8666192 0.8075293
## 23: 2 ORF39 0.7048446 0.8666192 0.8075293
## 24: 2 ORF40 0.7048446 0.8666192 0.8075293
## 25: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 26: 2 ORF45, ORF46 0.7048446 0.8666192 0.8075293
## 27: 3 ORF3 0.9968786 0.9990302 0.9826369
## 28: 3 ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 29: 3 ORF22 0.9968786 0.9990302 0.9826369
## 30: 3 ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 31: 3 ORF37 0.9968786 0.9990302 0.9826369
## 32: 3 CTO 0.9968786 0.9990302 0.9826369
## 33: 3 ORF44 0.9968786 0.9990302 0.9826369
## 34: 3 ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 35: 3 ORF66_1 0.9968786 0.9990302 0.9826369
## 36: 4 ORF4 0.2153731 0.6088215 0.6060342
## 37: 4 ORF31 0.2153731 0.6088215 0.6060342
## 38: 4 ORF65_1 0.2153731 0.6088215 0.6060342
## 39: 4 ORF68, ORF67_1 0.2153731 0.6088215 0.6060342
## 40: 4 ORF69, ORF70 0.2153731 0.6088215 0.6060342
## 41: 5 ORF18, ORF17, ORF16, ORF15 0.2097334 0.6269125 0.5728833
## 42: 5 ORF19 0.2097334 0.6269125 0.5728833
## 43: 5 ORF52 0.2097334 0.6269125 0.5728833
## 44: 5 ORF57, ORF58 0.2097334 0.6269125 0.5728833
## 45: 5 ORF71, ORF72, ORF73 0.2097334 0.6269125 0.5728833
## 46: 6 ORF53, ORF54 0.9902010 0.9978135 0.9076866
## 47: 7 ORF64_1 0.6046887 0.8596618 0.6312348
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 7: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 8: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 9: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 10: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 11: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 12: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 13: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 14: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 15: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 16: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 17: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 18: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 19: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 20: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 21: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 22: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 23: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 24: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 25: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 26: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 27: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 28: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 29: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 30: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 31: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 32: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 33: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 34: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 35: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 36: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 37: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 38: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 39: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 40: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 41: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 42: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 43: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 44: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 45: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 46: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 47: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## se.si se.au se.bp v c pchi
## [1] "ORF74, ORF75, ORF76, ORF67 _2"## [1] 1## [1] "ORF2" "ORF8"
## [3] "ORF23" "ORF24"
## [5] "ORF27, ORF26, ORF25" "ORF37, ORF36, ORF35, ORF35.5"
## [7] "ORF36" "ORF39"
## [9] "ORF40" "ORF41, ORF42, OF43"
## [11] "ORF45, ORF46" "ORF4"
## [13] "ORF31" "ORF65_1"
## [15] "ORF68, ORF67_1" "ORF69, ORF70"
## [17] "ORF18, ORF17, ORF16, ORF15" "ORF19"
## [19] "ORF52" "ORF57, ORF58"
## [21] "ORF71, ORF72, ORF73" "ORF64_1"## [1] 22Clustering statistics: Cluster number: 10
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF17 1.0000000 1.0000000 1.0000000
## 4: 1 ORF30 1.0000000 1.0000000 1.0000000
## 5: 1 ORF63 1.0000000 1.0000000 1.0000000
## 6: 2 ORF2 0.7048446 0.8666192 0.8075293
## 7: 2 ORF8 0.7048446 0.8666192 0.8075293
## 8: 2 ORF23 0.7048446 0.8666192 0.8075293
## 9: 2 ORF24 0.7048446 0.8666192 0.8075293
## 10: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 11: 2 ORF36 0.7048446 0.8666192 0.8075293
## 12: 2 ORF40 0.7048446 0.8666192 0.8075293
## 13: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 14: 3 ORF3 0.9968786 0.9990302 0.9826369
## 15: 3 ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 16: 3 ORF22 0.9968786 0.9990302 0.9826369
## 17: 3 ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 18: 3 ORF37 0.9968786 0.9990302 0.9826369
## 19: 3 CTO 0.9968786 0.9990302 0.9826369
## 20: 3 ORF44 0.9968786 0.9990302 0.9826369
## 21: 3 ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 22: 3 ORF66_1 0.9968786 0.9990302 0.9826369
## 23: 4 ORF4 0.2153731 0.6088215 0.6060342
## 24: 4 ORF31 0.2153731 0.6088215 0.6060342
## 25: 4 ORF65_1 0.2153731 0.6088215 0.6060342
## 26: 4 ORF68, ORF67_1 0.2153731 0.6088215 0.6060342
## 27: 4 ORF69, ORF70 0.2153731 0.6088215 0.6060342
## 28: 5 ORF9 0.2097334 0.6269125 0.5728833
## 29: 5 ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 30: 5 ORF18 0.2097334 0.6269125 0.5728833
## 31: 5 ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 32: 5 ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 33: 5 ORF38 0.2097334 0.6269125 0.5728833
## 34: 5 ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 35: 5 NOIR_1 0.2097334 0.6269125 0.5728833
## 36: 5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 37: 5 NOIR_2 0.2097334 0.6269125 0.5728833
## 38: 6 ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 39: 7 ORF19 0.6046887 0.8596618 0.6312348
## 40: 7 ORF52 0.6046887 0.8596618 0.6312348
## 41: 7 ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 42: 7 ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 43: 8 ORF27, ORF26, ORF25 0.9713771 0.9899227 0.9410908
## 44: 8 ORF39 0.9713771 0.9899227 0.9410908
## 45: 8 ORF45, ORF46 0.9713771 0.9899227 0.9410908
## 46: 9 ORF53, ORF54 0.9581874 0.9844445 0.9335398
## 47: 10 ORF64_1 0.7865513 0.9466014 0.6044383
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 25: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 26: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 27: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 35: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 36: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 37: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 38: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 39: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 40: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 41: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 42: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 43: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 44: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 45: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 46: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 47: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
## se.si se.au se.bp v c pchi
## [1] "ORF74, ORF75, ORF76, ORF67 _2"## [1] 1## [1] "ORF2" "ORF8"
## [3] "ORF23" "ORF24"
## [5] "ORF37, ORF36, ORF35, ORF35.5" "ORF36"
## [7] "ORF40" "ORF41, ORF42, OF43"
## [9] "ORF4" "ORF31"
## [11] "ORF65_1" "ORF68, ORF67_1"
## [13] "ORF69, ORF70" "ORF9"
## [15] "ORF10, ORF11" "ORF18"
## [17] "ORF22, ORF21, ORF20" "ORF32, ORF33, ORF34"
## [19] "ORF38" "ORF48, ORF49, ORF50, ORF51"
## [21] "NOIR_1" "ORF74, ORF75, ORF76, ORF67 _2"
## [23] "NOIR_2" "ORF19"
## [25] "ORF52" "ORF57, ORF58"
## [27] "ORF71, ORF72, ORF73" "ORF64_1"## [1] 28Clustering statistics: Cluster number: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF17 1.0000000 1.0000000 1.0000000
## 4: 1 ORF30 1.0000000 1.0000000 1.0000000
## 5: 1 ORF63 1.0000000 1.0000000 1.0000000
## 6: 2 ORF2 0.7048446 0.8666192 0.8075293
## 7: 2 ORF8 0.7048446 0.8666192 0.8075293
## 8: 2 ORF23 0.7048446 0.8666192 0.8075293
## 9: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 10: 2 ORF36 0.7048446 0.8666192 0.8075293
## 11: 2 ORF40 0.7048446 0.8666192 0.8075293
## 12: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 13: 3 ORF3 0.9968786 0.9990302 0.9826369
## 14: 3 ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 15: 3 ORF22 0.9968786 0.9990302 0.9826369
## 16: 3 ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 17: 3 ORF37 0.9968786 0.9990302 0.9826369
## 18: 3 CTO 0.9968786 0.9990302 0.9826369
## 19: 3 ORF44 0.9968786 0.9990302 0.9826369
## 20: 3 ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 21: 3 ORF66_1 0.9968786 0.9990302 0.9826369
## 22: 4 ORF4 0.2153731 0.6088215 0.6060342
## 23: 4 ORF31 0.2153731 0.6088215 0.6060342
## 24: 5 ORF9 0.2097334 0.6269125 0.5728833
## 25: 5 ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 26: 5 ORF18 0.2097334 0.6269125 0.5728833
## 27: 5 ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 28: 5 ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 29: 5 ORF38 0.2097334 0.6269125 0.5728833
## 30: 5 ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 31: 5 NOIR_1 0.2097334 0.6269125 0.5728833
## 32: 5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 33: 5 NOIR_2 0.2097334 0.6269125 0.5728833
## 34: 6 ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 35: 7 ORF19 0.6046887 0.8596618 0.6312348
## 36: 7 ORF52 0.6046887 0.8596618 0.6312348
## 37: 7 ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 38: 7 ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 39: 8 ORF24 0.9713771 0.9899227 0.9410908
## 40: 9 ORF27, ORF26, ORF25 0.9581874 0.9844445 0.9335398
## 41: 9 ORF39 0.9581874 0.9844445 0.9335398
## 42: 9 ORF45, ORF46 0.9581874 0.9844445 0.9335398
## 43: 10 ORF53, ORF54 0.7865513 0.9466014 0.6044383
## 44: 11 ORF64_1 0.9397368 0.9807196 0.8714120
## 45: 12 ORF65_1 0.4822671 0.8939242 0.3442378
## 46: 12 ORF68, ORF67_1 0.4822671 0.8939242 0.3442378
## 47: 12 ORF69, ORF70 0.4822671 0.8939242 0.3442378
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 25: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 26: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 27: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 35: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 36: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 37: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 38: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 39: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 40: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 41: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 42: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 43: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
## 44: 0.010922854 0.0043986223 0.003738478 -1.6009673 0.467876036 0.71047807
## 45: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 46: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 47: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## se.si se.au se.bp v c pchi
## [1] "ORF3" "ORF74, ORF75, ORF76, ORF67 _2"## [1] 2## [1] "ORF2" "ORF8"
## [3] "ORF23" "ORF37, ORF36, ORF35, ORF35.5"
## [5] "ORF36" "ORF40"
## [7] "ORF41, ORF42, OF43" "ORF4"
## [9] "ORF31" "ORF9"
## [11] "ORF10, ORF11" "ORF18"
## [13] "ORF22, ORF21, ORF20" "ORF32, ORF33, ORF34"
## [15] "ORF38" "ORF48, ORF49, ORF50, ORF51"
## [17] "NOIR_1" "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2" "ORF19"
## [21] "ORF52" "ORF57, ORF58"
## [23] "ORF71, ORF72, ORF73" "ORF53, ORF54"
## [25] "ORF65_1" "ORF68, ORF67_1"
## [27] "ORF69, ORF70"## [1] 27Selected number of clusters: 12
## Key: <cluster>
## cluster gene si au bp
## <int> <char> <num> <num> <num>
## 1: 1 ORF1 1.0000000 1.0000000 1.0000000
## 2: 1 ORF7, ORF6, ORF5 1.0000000 1.0000000 1.0000000
## 3: 1 ORF17 1.0000000 1.0000000 1.0000000
## 4: 1 ORF30 1.0000000 1.0000000 1.0000000
## 5: 1 ORF63 1.0000000 1.0000000 1.0000000
## 6: 2 ORF2 0.7048446 0.8666192 0.8075293
## 7: 2 ORF8 0.7048446 0.8666192 0.8075293
## 8: 2 ORF23 0.7048446 0.8666192 0.8075293
## 9: 2 ORF37, ORF36, ORF35, ORF35.5 0.7048446 0.8666192 0.8075293
## 10: 2 ORF36 0.7048446 0.8666192 0.8075293
## 11: 2 ORF40 0.7048446 0.8666192 0.8075293
## 12: 2 ORF41, ORF42, OF43 0.7048446 0.8666192 0.8075293
## 13: 3 ORF3 0.9968786 0.9990302 0.9826369
## 14: 3 ORF12, ORF13, ORF14 0.9968786 0.9990302 0.9826369
## 15: 3 ORF22 0.9968786 0.9990302 0.9826369
## 16: 3 ORF28, ORF29 0.9968786 0.9990302 0.9826369
## 17: 3 ORF37 0.9968786 0.9990302 0.9826369
## 18: 3 CTO 0.9968786 0.9990302 0.9826369
## 19: 3 ORF44 0.9968786 0.9990302 0.9826369
## 20: 3 ORF62, ORF61, ORF60,ORF59 0.9968786 0.9990302 0.9826369
## 21: 3 ORF66_1 0.9968786 0.9990302 0.9826369
## 22: 4 ORF4 0.2153731 0.6088215 0.6060342
## 23: 4 ORF31 0.2153731 0.6088215 0.6060342
## 24: 5 ORF9 0.2097334 0.6269125 0.5728833
## 25: 5 ORF10, ORF11 0.2097334 0.6269125 0.5728833
## 26: 5 ORF18 0.2097334 0.6269125 0.5728833
## 27: 5 ORF22, ORF21, ORF20 0.2097334 0.6269125 0.5728833
## 28: 5 ORF32, ORF33, ORF34 0.2097334 0.6269125 0.5728833
## 29: 5 ORF38 0.2097334 0.6269125 0.5728833
## 30: 5 ORF48, ORF49, ORF50, ORF51 0.2097334 0.6269125 0.5728833
## 31: 5 NOIR_1 0.2097334 0.6269125 0.5728833
## 32: 5 ORF74, ORF75, ORF76, ORF67 _2 0.2097334 0.6269125 0.5728833
## 33: 5 NOIR_2 0.2097334 0.6269125 0.5728833
## 34: 6 ORF18, ORF17, ORF16, ORF15 0.9902010 0.9978135 0.9076866
## 35: 7 ORF19 0.6046887 0.8596618 0.6312348
## 36: 7 ORF52 0.6046887 0.8596618 0.6312348
## 37: 7 ORF57, ORF58 0.6046887 0.8596618 0.6312348
## 38: 7 ORF71, ORF72, ORF73 0.6046887 0.8596618 0.6312348
## 39: 8 ORF24 0.9713771 0.9899227 0.9410908
## 40: 9 ORF27, ORF26, ORF25 0.9581874 0.9844445 0.9335398
## 41: 9 ORF39 0.9581874 0.9844445 0.9335398
## 42: 9 ORF45, ORF46 0.9581874 0.9844445 0.9335398
## 43: 10 ORF53, ORF54 0.7865513 0.9466014 0.6044383
## 44: 11 ORF64_1 0.9397368 0.9807196 0.8714120
## 45: 12 ORF65_1 0.4822671 0.8939242 0.3442378
## 46: 12 ORF68, ORF67_1 0.4822671 0.8939242 0.3442378
## 47: 12 ORF69, ORF70 0.4822671 0.8939242 0.3442378
## cluster gene si au bp
## se.si se.au se.bp v c pchi
## <num> <num> <num> <num> <num> <num>
## 1: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 2: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 3: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 4: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 5: 0.000000000 0.0000000000 0.000000000 0.0000000 0.000000000 0.00000000
## 6: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 7: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 8: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 9: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 10: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 11: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 12: 0.030713183 0.0184804288 0.004242426 -0.9896894 0.120861773 0.04360466
## 13: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 14: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 15: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 16: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 17: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 18: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 19: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 20: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 21: 0.001666092 0.0005998496 0.001787883 -2.6054330 0.493895884 0.51552261
## 22: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 23: 0.036986256 0.0296683840 0.005158657 -0.2726231 0.003625631 0.28835974
## 24: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 25: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 26: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 27: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 28: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 29: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 30: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 31: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 32: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 33: 0.037831759 0.0290755228 0.005221783 -0.2537033 0.069983618 0.19836467
## 34: 0.002579415 0.0007069161 0.003382598 -2.0882802 0.761636977 0.66855030
## 35: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 36: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 37: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 38: 0.033913009 0.0173493850 0.005130924 -0.7069634 0.371837861 0.22735153
## 39: 0.007210778 0.0030682248 0.002713877 -1.9437261 0.379729601 0.68951670
## 40: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 41: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 42: 0.009463766 0.0042823500 0.002828574 -1.8291668 0.326482429 0.14493668
## 43: 0.024161551 0.0085155497 0.005221713 -0.9388047 0.673952525 0.43119744
## 44: 0.010922854 0.0043986223 0.003738478 -1.6009673 0.467876036 0.71047807
## 45: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 46: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## 47: 0.045705473 0.0150728631 0.005000637 -0.4233731 0.824297722 0.82089729
## se.si se.au se.bp v c pchi
## [1] "ORF3" "ORF74, ORF75, ORF76, ORF67 _2"## [1] 2## [1] "ORF2" "ORF8"
## [3] "ORF23" "ORF37, ORF36, ORF35, ORF35.5"
## [5] "ORF36" "ORF40"
## [7] "ORF41, ORF42, OF43" "ORF4"
## [9] "ORF31" "ORF9"
## [11] "ORF10, ORF11" "ORF18"
## [13] "ORF22, ORF21, ORF20" "ORF32, ORF33, ORF34"
## [15] "ORF38" "ORF48, ORF49, ORF50, ORF51"
## [17] "NOIR_1" "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2" "ORF19"
## [21] "ORF52" "ORF57, ORF58"
## [23] "ORF71, ORF72, ORF73" "ORF53, ORF54"
## [25] "ORF65_1" "ORF68, ORF67_1"
## [27] "ORF69, ORF70"## [1] 27Remove genes from clusters ?
## [1] "ORF2" "ORF8"
## [3] "ORF23" "ORF37, ORF36, ORF35, ORF35.5"
## [5] "ORF36" "ORF40"
## [7] "ORF41, ORF42, OF43" "ORF4"
## [9] "ORF31" "ORF9"
## [11] "ORF10, ORF11" "ORF18"
## [13] "ORF22, ORF21, ORF20" "ORF32, ORF33, ORF34"
## [15] "ORF38" "ORF48, ORF49, ORF50, ORF51"
## [17] "NOIR_1" "ORF74, ORF75, ORF76, ORF67 _2"
## [19] "NOIR_2" "ORF19"
## [21] "ORF52" "ORF57, ORF58"
## [23] "ORF71, ORF72, ORF73" "ORF53, ORF54"
## [25] "ORF65_1" "ORF68, ORF67_1"
## [27] "ORF69, ORF70"## [1] 27## No genes were removed from their corresponding clusters.## cluster N
## <int> <int>
## 1: 5 10
## 2: 3 9
## 3: 2 7
## 4: 1 5
## 5: 7 4
## 6: 9 3
## 7: 12 3
## 8: 4 2
## 9: 6 1
## 10: 8 1
## 11: 10 1
## 12: 11 1Merge cluster stats
Assigning genes to clusters
Summarize and melt
Heatmaps
Normalized Expression
Expression delta ~ 6 hpi
Z-score of expression delta ~ 6 hpi
ORF kinetics, according to literature-based kinetic classes
Barplot of mean and SD
Figure 4 REVIEW - Mean and SD with linear connection
Mean and SD with loess function
Mean and SD with linear connection - Figure 4
Each replicate with loess
ORF kinetics, according to de-novo kinetic classes
Mean and SD with linear connection
Figure 5 REVIEW - Mean and SD with linear connection
Compare literature and de novo kinetic classes
NA shows the number of genes where the clustering did not yield an unambiguous result.
Combined Kinetic classes
De Novo Clusters
Literature clusters
